The hPDB package

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Warnings:

Protein Data Bank file format is a most popular format for holding biological macromolecular data.

This is a very fast sequential parser:

In its parallel incarnation it is most probably the fastest parser for PDB format.

It is aimed to not only deliver event-based interface, but also a high-level data structure for manipulating data in spirit of BioPython's PDB parser.

hPDB - Haskell library for processing atomic biomolecular structures in Protein Data Bank format - Michal Jan Gajda. BMC Research Notes 2013, 6:483.


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Properties

Versions0.99, 0.999, 0.9999, 0.9999.1, 1.0, 1.1, 1.1, 1.1.1, 1.1.2, 1.2.0, 1.2.0.1, 1.2.0.2, 1.2.0.3, 1.2.0.4, 1.2.0.5, 1.2.0.6, 1.2.0.7, 1.2.0.8, 1.2.0.9
Change logNone available
DependenciesAC-Vector, base (>=4.0 && <4.8), bytestring, containers, deepseq, directory, ghc-prim, iterable (>=2.0), mmap, mtl, Octree (>=0.5), parallel (>=3.0.0.0), QuickCheck (>=2.5.0.0), template-haskell, text (>=0.11.1.13), text-format (>=0.3.1.0), vector, zlib [details]
LicenseBSD3
CopyrightCopyright by Michal J. Gajda '2009-'2013
AuthorMichal J. Gajda
Maintainermjgajda@googlemail.com
CategoryBioinformatics
Home pagehttps://github.com/BioHaskell/hPDB
Bug trackermailto:mjgajda@googlemail.com
Source repositoryhead: git clone https://github.com/BioHaskell/hPDB
head: git clone git://github.com:mgajda/hpdb.git
UploadedSun Dec 8 19:07:01 UTC 2013 by MichalGajda

Modules

Flags

NameDescriptionDefaultType
have-mmapUse mmap to read input faster.EnabledAutomatic
have-sse2Use -msse2 for faster code.EnabledAutomatic
have-text-formatDo not use text-format, since it may require double-conversion and thus linking of libstdc++ which may break compilation due to GHC bug #5289: http://ghc.haskell.org/trac/ghc/ticket/5289EnabledAutomatic
old-bytestringUse bytestring before version 0.10 (introduced in GHC 7.6), and define NFData for Data.ByteString yourself. Disable for GHC 7.6.DisabledAutomatic
old-zlibUse zlib before version 0.5.4 (introduced in GHC 7.6). Disable for GHC 7.6.1DisabledAutomatic
old-vectorUse old vector library before version 0.10 (introduced along with GHC 7.6). Disable for GHC 7.6.1 and latest 7.4.2.DisabledAutomatic

Use -f <flag> to enable a flag, or -f -<flag> to disable that flag. More info

Downloads

Maintainers' corner

For package maintainers and hackage trustees

Readme for hPDB-1.1

hPDB

Haskell PDB file format parser.

Build Status

Protein Data Bank file format is a most popular format for holding biomolecule data.

This is a very fast parser:

It is aimed to not only deliver event-based interface, but also a high-level data structure for manipulating data in spirit of BioPython's PDB parser.

Details on official releases are on Hackage.